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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ), 'gf_id' => 'HOM05D001170', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001170' ), 'data_identifier' => 'HOM05D001170', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001170', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '530', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38430' => 'bna', 'A03p21110' => 'bna', 'A03p30250' => 'bna', 'A05p33760' => 'bna', 'A07p22310' => 'bna', 'A09p25950' => 'bna', 'A09p25960' => 'bna', 'A09p47840' => 'bna', 'Aa31LG5G23190' => 'aar', 'Aa31LG8G2860' => 'aar', 'Aa31LG9G9540' => 'aar', 'Aa31sc43G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.376' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2023' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1900' => 'aag', 'Actinidia01886' => 'ach', 'Actinidia05360' => 'ach', 'Actinidia05624' => 'ach', 'Actinidia19534' => 'ach', 'Actinidia28998' => 'ach', 'Ah.03g136480' => 'amhyb', 'Ah.05g170000' => 'amhyb', 'Ah.14g089410' => 'amhyb', 'AL1G49430' => 'aly', 'AL3G28320' => 'aly', 'AL3G40870' => 'aly', 'AL4G35310' => 'aly', 'AL4G35350' => 'aly', 'AL5G36010' => 'aly', 'AL6G48460' => 'aly', 'Aqoxy1G02463' => 'aox', 'Aqoxy1G03999' => 'aox', 'Aqoxy4G00926' => 'aox', 'Aqoxy4G02521' => 'aox', 'Aqoxy5G02903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18IZSC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.25IQBC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SZ21F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5F4UJS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU1MR9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FN1A8Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NX47XU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S2R1T1' => 'arhy', 'AT2G38270' => 'ath', 'AT3G15660' => 'ath', 'AT3G54900' => 'ath', 'AT4G04950' => 'ath', 'AT4G32580' => 'ath', 'ATR0582G248' => 'atr', 'ATR0680G019' => 'atr', 'ATR0681G276' => 'atr', 'ATR0724G012' => 'atr', 'ATR0724G071' => 'atr', 'ATR0767G165' => 'atr', 'Atru.chr1.3105' => 'acertr', 'Atru.chr10.1898' => 'acertr', 'Atru.chr6.2748' => 'acertr', 'Atru.chr8.2265' => 'acertr', 'AUR62003247' => 'cqu', 'AUR62014807' => 'cqu', 'AUR62016999' => 'cqu', 'AUR62027223' => 'cqu', 'AUR62027755' => 'cqu', 'AUR62030484' => 'cqu', 'AUR62030807' => 'cqu', 'AUR62038520' => 'cqu', 'BcaB01g00148' => 'bca', 'BcaB01g01849' => 'bca', 'BcaB01g03712' => 'bca', 'BcaB01g05292' => 'bca', 'BcaB02g07714' => 'bca', 'BcaB04g20909' => 'bca', 'BcaC01g05553' => 'bca', 'BcaC02g08216' => 'bca', 'BcaC04g21350' => 'bca', 'BcaC07g39768' => 'bca', 'BcaC08g44706' => 'bca', 'BcaC09g48547' => 'bca', 'BcaC09g51498' => 'bca', 'BolC1t04829H' => 'bol', 'BolC3t14891H' => 'bol', 'BolC3t15963H' => 'bol', 'BolC6t37427H' => 'bol', 'BolC8t50618H' => 'bol', 'BolC9t56125H' => 'bol', 'BraA01t03893Z' => 'bra', 'BraA03t11352Z' => 'bra', 'BraA03t12209Z' => 'bra', 'BraA05t22199Z' => 'bra', 'BraA07t29909Z' => 'bra', 'BraA09t38163Z' => 'bra', 'BraA09t40241Z' => 'bra', 'C01p48740' => 'bna', 'C03p25000' => 'bna', 'C03p36500' => 'bna', 'C05p50770' => 'bna', 'C06p22400' => 'bna', 'C08p30090' => 'bna', 'C09p32880' => 'bna', 'C09p32900' => 'bna', 'CAN.G1164.19' => 'can', 'CAN.G133.10' => 'can', 'CAN.G395.44' => 'can', 'CAN.G809.5' => 'can', 'CANSAT35G0043' => 'cansat', 'CANSAT54G1807' => 'cansat', 'CANSAT64G0395' => 'cansat', 'CANSAT80G1846' => 'cansat', 'CARHR090750' => 'chi', 'CARHR132850' => 'chi', 'CARHR164890' => 'chi', 'CARHR252590' => 'chi', 'Carub.0003s1541' => 'cru', 'Carub.0004s2022' => 'cru', 'Carub.0005s2151' => 'cru', 'Carub.0006s3288' => 'cru', 'Ca_01086_v3' => 'car', 'Ca_18539_v3' => 'car', 'CBR_g22937' => 'cbr', 'CBR_g35003' => 'cbr', 'CBR_g41800' => 'cbr', 'Cc02_g13250' => 'ccan', 'Cc04_g03980' => 'ccan', 'Cc05_g02070' => 'ccan', 'Cc06_g01160' => 'ccan', 'Cc07_g01480' => 'ccan', 'CDE01G0177' => 'cde', 'CDE04G1642' => 'cde', 'CDE06G1919' => 'cde', 'CDE06G1991' => 'cde', 'CDE06G2620' => 'cde', 'CDE09G0376' => 'cde', 'CDE12G0548' => 'cde', 'Cfa000433' => 'cfa', 'Cfa006281' => 'cfa', 'Cfa010927' => 'cfa', 'Cfa017188' => 'cfa', 'Cfa024358' => 'cfa', 'Ciclev10012321m.g' => 'ccl', 'Ciclev10015059m.g' => 'ccl', 'Ciclev10016894m.g' => 'ccl', 'Ciclev10026629m.g' => 'ccl', 'CiPaw.01G244000' => 'cil', 'CiPaw.08G116300' => 'cil', 'CiPaw.09G058800' => 'cil', 'CiPaw.09G210900' => 'cil', 'CiPaw.10G047600' => 'cil', 'ClCG01G022920' => 'cla', 'ClCG10G010110' => 'cla', 'ClCG10G022280' => 'cla', 'ClCG11G010980' => 'cla', 'COL.COLO4_06601' => 'col', 'COL.COLO4_12888' => 'col', 'COL.COLO4_31488' => 'col', 'Cpa.g.sc10.223' => 'cpa', 'Cpa.g.sc11.97' => 'cpa', 'Cpa.g.sc27.48' => 'cpa', 'Cre01.g047800' => 'cre', 'Cre04.g232602' => 'cre', 'Cre07.g325600' => 'cre', 'Cre07.g325743' => 'cre', 'CsaV3_2G009510' => 'csa', 'CsaV3_3G033600' => 'csa', 'CsaV3_4G001380' => 'csa', 'CsaV3_6G050090' => 'csa', 'CSS0009163' => 'camsi', 'CSS0009287' => 'camsi', 'CSS0009561' => 'camsi', 'CSS0013622' => 'camsi', 'CSS0016276' => 'camsi', 'CSS0022165' => 'camsi', 'CSS0022469' => 'camsi', 'CSS0022827' => 'camsi', 'CSS0029114' => 'camsi', 'CSS0032119' => 'camsi', 'CSS0032266' => 'camsi', 'CSS0038997' => 'camsi', 'CSS0043406' => 'camsi', 'CSS0045002' => 'camsi', 'CSS0049641' => 'camsi', 'DCAR_000959' => 'dca', 'DCAR_004078' => 'dca', 'DCAR_018690' => 'dca', 'DCAR_021328' => 'dca', 'Dinv07552' => 'din', 'Dinv09288' => 'din', 'Dinv11584' => 'din', 'Dinv30210' => 'din', 'Dinv33255' => 'din', 'Dinv40547' => 'din', 'Duzib093G1404' => 'dzi', 'Duzib128G0294' => 'dzi', 'Duzib192G0175' => 'dzi', 'Duzib192G0182' => 'dzi', 'Duzib235G1347' => 'dzi', 'ECA234G3104' => 'eca', 'ECA236G0793' => 'eca', 'ECA236G1805' => 'eca', 'ECA238G2587' => 'eca', 'ECA246G2008' => 'eca', 'ECA248G2451' => 'eca', 'EL10Ac1g01218' => 'bvu', 'EL10Ac6g13924' => 'bvu', 'EL10Ac8g20369' => 'bvu', 'Eucgr.D00629' => 'egr', 'Eucgr.D00987' => 'egr', 'Eucgr.D00992' => 'egr', 'Eucgr.D00994' => 'egr', 'Eucgr.I01560' => 'egr', 'Eucgr.K02975' => 'egr', 'FAN02G4334' => 'fan', 'FAN02G4623' => 'fan', 'FAN05G3026' => 'fan', 'FAN09G0318' => 'fan', 'FAN09G1422' => 'fan', 'FAN09G3438' => 'fan', 'FAN11G2442' => 'fan', 'FAN14G1569' => 'fan', 'FAN14G2338' => 'fan', 'FAN14G4496' => 'fan', 'FAN16G0881' => 'fan', 'FAN21G0582' => 'fan', 'FAN25G3150' => 'fan', 'FvH4_3g09370' => 'fve', 'FvH4_6g00720' => 'fve', 'FvH4_6g11240' => 'fve', 'FvH4_6g30390' => 'fve', 'Glyma.01G119900' => 'gma', 'Glyma.03G056300' => 'gma', 'Glyma.07G032600' => 'gma', 'Glyma.08G209900' => 'gma', 'Glyma.09G252200' => 'gma', 'Glyma.13G180400' => 'gma', 'Glyma.13G363100' => 'gma', 'Glyma.18G240400' => 'gma', 'Gohir.A09G166100' => 'ghi', 'Gohir.A10G025200' => 'ghi', 'Gohir.A10G076500' => 'ghi', 'Gohir.A11G020200' => 'ghi', 'Gohir.D09G161700' => 'ghi', 'Gohir.D10G025900' => 'ghi', 'Gohir.D10G074800' => 'ghi', 'Gohir.D11G019900' => 'ghi', 'Gorai.006G183400' => 'gra', 'Gorai.007G021200' => 'gra', 'Gorai.011G027200' => 'gra', 'Gorai.011G080700' => 'gra', 'GSVIVG01002064001' => 'vvi', 'GSVIVG01011178001' => 'vvi', 'GSVIVG01017244001' => 'vvi', 'GSVIVG01032936001' => 'vvi', 'HanXRQChr04g0124081' => 'han', 'HanXRQChr10g0304481' => 'han', 'HanXRQChr11g0331711' => 'han', 'HanXRQChr14g0451571' => 'han', 'HanXRQChr16g0504211' => 'han', 'Haze_03014' => 'cav', 'Haze_03021' => 'cav', 'Haze_04529' => 'cav', 'Haze_06482' => 'cav', 'Haze_20986' => 'cav', 'Haze_26315' => 'cav', 'Haze_27646' => 'cav', 'Hma1.2p1_0126F.1_g059340' => 'hma', 'Hma1.2p1_0126F.1_g059350' => 'hma', 'Hma1.2p1_0362F.1_g136420' => 'hma', 'Hma1.2p1_0421F.1_g149800' => 'hma', 'Hma1.2p1_0421F.1_g149810' => 'hma', 'Hma1.2p1_0515F.1_g170270' => 'hma', 'HPP92_006344' => 'vpl', 'HPP92_019010' => 'vpl', 'HPP92_022713' => 'vpl', 'Hund10990' => 'sun', 'Hund21229' => 'sun', 'Lalb_Chr03g0038351' => 'lal', 'Lalb_Chr05g0218421' => 'lal', 'Lalb_Chr07g0192391' => 'lal', 'Lalb_Chr22g0351021' => 'lal', 'Lj1A1206T69' => 'lonja', 'Lj1g0025103' => 'lja', 'Lj2A397T24' => 'lonja', 'Lj2A397T25' => 'lonja', 'Lj2A72T46' => 'lonja', 'Lj3g0003704' => 'lja', 'Lj3g0006687' => 'lja', 'Lj3g0006921' => 'lja', 'Lj3g0007470' => 'lja', 'Lj4g0016173' => 'lja', 'Lj5A68T68' => 'lonja', 'Lj7P620T26' => 'lonja', 'Lsat_1_v5_gn_1_37260' => 'lsa', 'Lsat_1_v5_gn_2_95140' => 'lsa', 'Lsat_1_v5_gn_6_117141' => 'lsa', 'Lsat_1_v5_gn_7_21060' => 'lsa', 'Lsat_1_v5_gn_8_101640' => 'lsa', 'Manes.04G095400' => 'mes', 'Manes.04G117000' => 'mes', 'Manes.08G093600' => 'mes', 'Manes.11G052500' => 'mes', 'Manes.16G026500' => 'mes', 'Mapoly0001s0103' => 'mpo', 'Mapoly0006s0309' => 'mpo', 'Mapoly0037s0022' => 'mpo', 'Mapoly0188s0015' => 'mpo', 'MBI01_g11878_MAGBIO' => 'mbi', 'MBI04_g29831_MAGBIO' => 'mbi', 'MBI11_g22250_MAGBIO' => 'mbi', 'MBI11_g35129_MAGBIO' => 'mbi', 'MBI15_g13301_MAGBIO' => 'mbi', 'MCO01G282' => 'mco', 'MCO03G072' => 'mco', 'MCO10G154' => 'mco', 'MCO10G282' => 'mco', 'MD00G1095700' => 'mdo', 'MD00G1172400' => 'mdo', 'MD04G1241900' => 'mdo', 'MD05G1313900' => 'mdo', 'MD12G1258800' => 'mdo', 'MD17G1204000' => 'mdo', 'Medtr2g103130' => 'mtr', 'Medtr4g016930' => 'mtr', 'Medtr4g088905' => 'mtr', 'Medtr7g079520' => 'mtr', 'MELO3C007287.2' => 'cme', 'MELO3C008750.2' => 'cme', 'MELO3C009150.2' => 'cme', 'MELO3C017902.2' => 'cme', 'Migut.B01277' => 'egut', 'Migut.F00004' => 'egut', 'Migut.L02023' => 'egut', 'Migut.M01149' => 'egut', 'MSTRG.18998' => 'ama', 'MSTRG.3033' => 'ama', 'MSTRG.334' => 'ama', 'Nitab4.5_0000261g0040' => 'nta', 'Nitab4.5_0000620g0090' => 'nta', 'Nitab4.5_0002158g0110' => 'nta', 'Nitab4.5_0003512g0090' => 'nta', 'Nitab4.5_0004411g0040' => 'nta', 'Nitab4.5_0011381g0010' => 'nta', 'Nitab4.5_0011717g0010' => 'nta', 'Nitab4.5_0013095g0010' => 'nta', 'Nn1g04056' => 'nnu', 'Nn2g10877' => 'nnu', 'Nn3g16178' => 'nnu', 'Nn3g16181' => 'nnu', 'Nn7g37528' => 'nnu', 'Oeu016099.1' => 'oeu', 'Oeu033463.1' => 'oeu', 'Oeu050843.2' => 'oeu', 'Oeu063396.1' => 'oeu', 'Os01g0174900' => 'osa', 'Os01g0530400' => 'osa', 'Os03g0851200' => 'osa', 'Os04g0568751' => 'osa', 'Os10g0500700' => 'osa', 'Os12g0175500' => 'osa', 'Peaxi162Scf00170g00007' => 'pax', 'Peaxi162Scf00170g00120' => 'pax', 'Peaxi162Scf00331g00001' => 'pax', 'Peaxi162Scf00404g00097' => 'pax', 'Peaxi162Scf00947g00115' => 'pax', 'PGR004G2504' => 'pgr', 'PGR031G0399' => 'pgr', 'PGR102G1290' => 'pgr', 'PGR142G0333' => 'pgr', 'PGSC0003DMG400004454' => 'stu', 'PGSC0003DMG400013635' => 'stu', 'PGSC0003DMG401028515' => 'stu', 'Phvul.002G228300' => 'pvu', 'Phvul.008G055800' => 'pvu', 'Phvul.010G075900' => 'pvu', 'Phvul.010G153500' => 'pvu', 'Potri.003G060600' => 'ptr', 'Potri.004G042200' => 'ptr', 'Potri.011G051400' => 'ptr', 'Potri.014G141200' => 'ptr', 'Potri.016G119200' => 'ptr', 'Pp3c10_4370' => 'ppa', 'Pp3c14_14790' => 'ppa', 'Pp3c14_3630' => 'ppa', 'Pp3c14_8810' => 'ppa', 'Pp3c24_14100' => 'ppa', 'Pp3c26_14030' => 'ppa', 'Pp3c3_2430' => 'ppa', 'Pp3c8_18520' => 'ppa', 'PRCOL_00004742' => 'pco', 'PRCOL_00004770' => 'pco', 'PRCOL_00004792' => 'pco', 'PRCOL_00005651' => 'pco', 'Prupe.1G187000' => 'ppe', 'Prupe.1G187400' => 'ppe', 'Prupe.3G079000' => 'ppe', 'Prupe.4G042200' => 'ppe', 'Prupe.4G045700' => 'ppe', 'Prupe.4G045800' => 'ppe', 'Prupe.6G279600' => 'ppe', 'Prupe.6G359300' => 'ppe', 'Prupe.8G067300' => 'ppe', 'Psat3g104200' => 'psa', 'Psat5g300480' => 'psa', 'Psat7g114400' => 'psa', 'PSO017G6205' => 'pso', 'PSO170G1001' => 'pso', 'PSO210G6149' => 'pso', 'PSO339G6149' => 'pso', 'PSO384G1831' => 'pso', 'PSO407G0198' => 'pso', 'PSO478G4380' => 'pso', 'PSO541G1004' => 'pso', 'PSO675G1931' => 'pso', 'QL05p040001' => 'qlo', 'QL07p015408' => 'qlo', 'QL07p035137' => 'qlo', 'QL12p006383' => 'qlo', 'RcHm_v2.0_Chr2g0136741' => 'rch', 'RcHm_v2.0_Chr3g0448191' => 'rch', 'RcHm_v2.0_Chr3g0462751' => 'rch', 'RcHm_v2.0_Chr5g0008221' => 'rch', 'Rhsim02G0062300' => 'rsi', 'Rhsim04G0126900' => 'rsi', 'Rhsim13G0177000' => 'rsi', 'Sabra03G0034800' => 'sbr', 'Sabra11G0035400' => 'sbr', 'Sabra14G0106500' => 'sbr', 'Sabra16G0115100' => 'sbr', 'SalBow4G1428' => 'sbo', 'SalBow5G2628' => 'sbo', 'SalBow5G4502' => 'sbo', 'SalBow7G0113' => 'sbo', 'SalBow8G0859' => 'sbo', 'Sc01g0006910' => 'sci', 'Sc07g0003420' => 'sci', 'Sc09g0002660' => 'sci', 'Sc24g0000960' => 'sci', 'Sed0007820' => 'sed', 'Sed0014265' => 'sed', 'Sed0018385' => 'sed', 'Sed0020397' => 'sed', 'SEGI_27167' => 'sgi', 'SEGI_32474' => 'sgi', 'SEGI_39266' => 'sgi', 'SGA_v2.0_scaffold100G29673' => 'sas', 'SGA_v2.0_scaffold173G39202' => 'sas', 'SGA_v2.0_scaffold39G15188' => 'sas', 'SGA_v2.0_scaffold40G15616' => 'sas', 'SHI01782' => 'shi', 'SHI32413' => 'shi', 'SMO141G0103' => 'smo', 'SMO196G0158' => 'smo', 'SMO307G0001' => 'smo', 'SMO307G0056' => 'smo', 'SMO340G0324' => 'smo', 'SMO347G0493' => 'smo', 'Solyc02g078360.4' => 'sly', 'Solyc02g082200.4' => 'sly', 'Solyc06g067960.3' => 'sly', 'Solyc09g005620.4' => 'sly', 'Sopen00g009970' => 'spe', 'Sopen02g023220' => 'spe', 'Sopen02g026860' => 'spe', 'Sopen06g025240' => 'spe', 'Sopen09g001520' => 'spe', 'Sp3g13960' => 'spa', 'Sp4g20550' => 'spa', 'Sp5g07530' => 'spa', 'Sp6g04010' => 'spa', 'TAR383G0630' => 'tar', 'TAR622G0119' => 'tar', 'TAR627G0846' => 'tar', 'TAR629G2507' => 'tar', 'TAR636G1119' => 'tar', 'THA.LOC104805920' => 'tha', 'THA.LOC104806287' => 'tha', 'THA.LOC104809971' => 'tha', 'THA.LOC104812862' => 'tha', 'THA.LOC104815538' => 'tha', 'THA.LOC104818039' => 'tha', 'THA.LOC104824236' => 'tha', 'Thecc.05G013600' => 'tca', 'Thecc.06G074000' => 'tca', 'Thecc.06G189200' => 'tca', 'Thecc.09G244600' => 'tca', 'Thhalv10010760m.g' => 'esa', 'Thhalv10017037m.g' => 'esa', 'Thhalv10021647m.g' => 'esa', 'Thhalv10028614m.g' => 'esa', 'TPR.G12036' => 'tpr', 'TPR.G203' => 'tpr', 'TPR.G20785' => 'tpr', 'TPR.G34421' => 'tpr', 'TPR.G36142' => 'tpr', 'TPR.G3661' => 'tpr', 'TPR.G37160' => 'tpr', 'TPR.G39440' => 'tpr', 'TPR.G40463' => 'tpr', 'TPR.G995' => 'tpr', 'TWI12G0482' => 'twi', 'TWI12G0603' => 'twi', 'TWI18G1279' => 'twi', 'TWI23G0202' => 'twi', 'TWI38G1016' => 'twi', 'TWI38G1622' => 'twi', 'TWI74G0526' => 'twi', 'unitig_22.g6228' => 'ugi', 'unitig_26.g9085' => 'ugi', 'unitig_26.g9275' => 'ugi', 'vmacro08884' => 'vma', 'vmacro15570' => 'vma', 'vmacro22107' => 'vma', 'vmacro22927' => 'vma', 'VMungo0251G3057' => 'vmu', 'VMungo0331G0578' => 'vmu', 'VMungo0331G1315' => 'vmu', 'Zm00001eb044380' => 'zma', 'Zm00001eb064590' => 'zma', 'Zm00001eb091680' => 'zma', 'Zm00001eb091690' => 'zma', 'Zm00001eb094310' => 'zma', 'Zm00001eb103590' => 'zma', 'Zm00001eb105530' => 'zma', 'Zm00001eb163210' => 'zma', 'Zm00001eb210730' => 'zma', 'Zm00001eb220880' => 'zma', 'Zm00001eb240990' => 'zma', 'Zm00001eb319160' => 'zma', 'Zm00001eb336840' => 'zma', 'Zm00001eb360150' => 'zma', 'Zm00001eb424600' => 'zma' ) $gf_id = 'HOM05D001170' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001170' ) $data_identifier = 'HOM05D001170' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 6, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 15, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'pco' => (int) 4, 'ppe' => (int) 9, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424600' $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